M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
LibreCat: https://research-explorer.ista.ac.at/record/10736
DOI: 10.7554/eLife.64543
WoS: 000751104400001
PMID: 35080492

I. Tomanek et al., “Gene amplification as a form of population-level gene expression regulation,” Nature Ecology &; Evolution, vol. 4, no. 4. Springer Nature, pp. 612–625, 2020.
LibreCat: https://research-explorer.ista.ac.at/record/7652
DOI: 10.1038/s41559-020-1132-7
WoS: 000519008300005

P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/423
DOI: 10.7554/eLife.32035
WoS: 000431035800001

P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/9840
DOI: 10.5061/dryad.42n44

C. Igler, M. Lagator, G. Tkadik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” Nature Ecology and Evolution, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/67
DOI: 10.1038/s41559-018-0651-y
WoS: 000447947600021

C. Igler, M. Lagator, G. Tkadik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.
LibreCat: https://research-explorer.ista.ac.at/record/5585
DOI: 10.15479/AT:ISTA:108

M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/570
DOI: 10.7554/eLife.28921

R. A. Fernandes Redondo, H. de Vladar, T. Wodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the =54 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/1077
DOI: 10.1098/rsif.2016.0139
WoS: 000393380400001

M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017.
LibreCat: https://research-explorer.ista.ac.at/record/954
DOI: 10.7554/eLife.25192
WoS: 000404024800001

M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/1427
DOI: 10.1093/molbev/msv269

R. A. Fernandes Redondo, H. de Vladar, T. Wodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the =54 phage family.” The Royal Society, 2016.
LibreCat: https://research-explorer.ista.ac.at/record/9864
DOI: 10.6084/m9.figshare.4315652.v1

A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014.
LibreCat: https://research-explorer.ista.ac.at/record/2042
DOI: 10.1186/1471-2164-15-663

A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/2412
DOI: 10.1186/1471-2148-13-54

R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG- infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/2410
DOI: 10.1128/genomeA.00216-13

M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
LibreCat: https://research-explorer.ista.ac.at/record/500
DOI: 10.1186/1471-2148-13-222

C. Guinane et al., “Evolutionary genomics of Staphylococcus aureus reveals insights into the origin and molecular basis of ruminant host adaptation,” Genome Biology and Evolution, vol. 2. Oxford University Press, pp. 454–466, 2010.
LibreCat: https://research-explorer.ista.ac.at/record/4358
DOI: 10.1093/gbe/evq031

J. P. Bollback and J. Huelsenbeck, “Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence,” Genetics, vol. 181, no. 1. Genetics Society of America, pp. 225–234, 2009.
LibreCat: https://research-explorer.ista.ac.at/record/4357
DOI: 10.1534/genetics.107.085225

J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of America, pp. 497–502, 2008.
LibreCat: https://research-explorer.ista.ac.at/record/3435
DOI: 10.1534/genetics.107.085019

J. Binladen et al., “The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing,” PLoS One, vol. 2, no. 2. Public Library of Science, 2007.
LibreCat: https://research-explorer.ista.ac.at/record/4353
DOI: 10.1371/journal.pone.0000197

L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes under positive selection in Escherichia coli,” Genome Research, vol. 17, no. 9. Cold Spring Harbor Laboratory Press, pp. 1336–1343, 2007.
LibreCat: https://research-explorer.ista.ac.at/record/4356
DOI: 10.1101/gr.6254707

J. P. Bollback and J. Huelsenbeck, “Clonal interference is alleviated by high mutation rates in large populations,” Molecular Biology and Evolution, vol. 24, no. 6. Oxford University Press, pp. 1397–1406, 2007.
LibreCat: https://research-explorer.ista.ac.at/record/4355
DOI: 10.1093/molbev/msm056

E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA,” Genome Research, vol. 17, no. 1. Cold Spring Harbor Laboratory Press, pp. 117–25, 2007.
LibreCat: https://research-explorer.ista.ac.at/record/4354
DOI: 10.1101/gr.5890907

S. Reynolds et al., “Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system,” The Auk, vol. 124, no. 3. University of California Press, pp. 857–867, 2007.
LibreCat: https://research-explorer.ista.ac.at/record/3436
DOI: 10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2

J. P. Bollback, P. Gardner, and R. Nielsen, “Estimating the history of mutations on a phylogeny,” in Ancestral Sequence Reconstruction, D. Liberles, Ed. Oxford University Press, 2007, pp. 69–79.
LibreCat: https://research-explorer.ista.ac.at/record/3432
DOI: 10.1093/acprof:oso/9780199299188.003.0006

J. Conn, J. Vineis, J. P. Bollback, D. Onyabe, R. Wilkerson, and M. Povoa, “Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil,” The American Journal of Tropical Medicine and Hygiene, vol. 74, no. 5. American Society of Tropical Medicine and Hygiene, pp. 798–806, 2006.
LibreCat: https://research-explorer.ista.ac.at/record/4352

J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.
LibreCat: https://research-explorer.ista.ac.at/record/4351
DOI: 10.1186/1471-2105-7-88

A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution,” Current Opinion in Genetics &; Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.
LibreCat: https://research-explorer.ista.ac.at/record/3437
DOI: 10.1016/j.gde.2006.10.006

J. P. Bollback, “Posterior mapping and posterior predictive distributions,” in Statistical methods in Molecular Evolution, R. Nielsen, Ed. Springer, 2005, pp. 439–462.
LibreCat: https://research-explorer.ista.ac.at/record/3433
DOI: 10.1007/0-387-27733-1

J. Harshman, C. Huddleston, J. P. Bollback, T. Parsons, and M. Braun, “True and false gharials: A nuclear gene phylogeny of crocodylia,” Systematic Biology, vol. 52, no. 3. Oxford University Press, pp. 386–402, 2003.
LibreCat: https://research-explorer.ista.ac.at/record/4350
DOI: 10.1080/10635150390197028
PMID:  12775527

J. Huelsenbeck, R. Nielsen, and J. P. Bollback, “Stochastic mapping of morphological characters,” Systematic Biology, vol. 52, no. 2. Oxford University Press, pp. 131–158, 2003.
LibreCat: https://research-explorer.ista.ac.at/record/4348
DOI: 10.1080/10635150390192780
PMID: 12746144 

J. P. Bollback, “Bayesian model adequacy and choice in phylogenetics,” Molecular Biology and Evolution, vol. 19, no. 7. Oxford University Press, pp. 1171–80, 2002.
LibreCat: https://research-explorer.ista.ac.at/record/4349
DOI: 10.1093/oxfordjournals.molbev.a004175
PMID: 12082136 

J. Huelsenbeck, J. P. Bollback, and A. Levine, “Inferring the root of a phylogenetic tree,” Systematic Biology, vol. 51, no. 1. Oxford University Press, pp. 32–43, 2002.
LibreCat: https://research-explorer.ista.ac.at/record/4347
DOI: 10.1080/106351502753475862
PMID: 11943091

J. P. Bollback and J. Huelsenbeck, “Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae),” Journal of Molecular Evolution, vol. 52, no. 2. Springer, pp. 117–128, 2001.
LibreCat: https://research-explorer.ista.ac.at/record/4229
DOI: 10.1007/s002390010140
PMID: 11231891

J. Conn, J. P. Bollback, D. Onyabe, T. Robinson, R. Wilkerson, and M. Povoa, “Isolation of polymorphic microsatellite markers from the malaria vector Anopheles darlingi,” Molecular Ecology Notes, vol. 1, no. 4. Wiley-Blackwell, pp. 223–225, 2001.
LibreCat: https://research-explorer.ista.ac.at/record/3439
DOI:  10.1046/j.1471-8278.2001.00078.x

J. Huelsenbeck and J. P. Bollback, “Empirical and hierarchical Bayesian estimation of ancestral states,” Systematic Biology, vol. 50, no. 3. Oxford University Press, pp. 351–366, 2001.
LibreCat: https://research-explorer.ista.ac.at/record/3440
DOI: 10.1080/10635150119871
PMID: 12116580

J. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback, “Bayesian inference of phylogeny and its impact on evolutionary biology,” Science, vol. 294, no. 5550. American Association for the Advancement of Science, pp. 2310–2314, 2001.
LibreCat: https://research-explorer.ista.ac.at/record/3438
DOI: 10.1126/science.1065889
PMID: 11743192 

J. Huelsenbeck and J. P. Bollback, “Application of the likelihood function in phylogenetic analysis,” in Handbook of Statistical Genetics, D. Balding, M. Bishop, and C. Cannings, Eds. Wiley-Blackwell, 2001, pp. 415–439.
LibreCat: https://research-explorer.ista.ac.at/record/3434
DOI: 10.1002/9780470061619.ch15